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Forum: Bioinformatics 03-16-2014, 07:40 PM
Replies: 0
Views: 1,142
Posted By Baoqing
VCFtools empty results for TajimaD calculation

Hi, I am trying to use the vcftools to get some summary statistics about my VCF file. The file is properly sorted and indexed. But, When I was using the following functions:

zcat my.sorted.vcf.gz...
Forum: Bioinformatics 03-10-2014, 09:09 AM
Replies: 1
Views: 1,296
Posted By Baoqing
never mind, i seemed to find the answer here,...

never mind, i seemed to find the answer here, sorry for the inconveniences
http://www.biostars.org/p/78444/
Forum: Bioinformatics 03-10-2014, 09:05 AM
Replies: 1
Views: 1,296
Posted By Baoqing
visualization of vcf in R

when i was trying to use R to visualize my VCF file I first loaded the file and compressed it:

vcf <- readVcf(str.vcf, "Genome")
compressVcf <- bgzip(vcf, tempfile())

but when i run...
Forum: Sample Prep / Library Generation 10-17-2013, 07:37 AM
Replies: 5
Views: 3,417
Posted By Baoqing
This response seems late, I had the exact same...

This response seems late, I had the exact same problem. I run a control of samples with RNA cleaned and uncleaned samples with picogreen. The untreated RNA samples reading was shooting to the roof....
Forum: RNA Sequencing 07-12-2013, 12:01 PM
Replies: 10
Views: 2,716
Posted By Baoqing
Thanks a lot! That worked brilliantly! I should...

Thanks a lot! That worked brilliantly! I should have explored the cummeRbund Package more. I resolved this by using :

samtools view sample_1_name_sorted.bam | htseq-count -i gene_id -...
Forum: Bioinformatics 06-22-2013, 08:41 PM
Replies: 21
Views: 11,899
Posted By Baoqing
sorry for the late response. can you at least...

sorry for the late response. can you at least load the library?
i found that if you had tried to read your data before the library properly loaded, the generated cuffData.db is going to intervene...
Forum: RNA Sequencing 06-21-2013, 10:59 PM
Replies: 3
Views: 1,455
Posted By Baoqing
p value is negative

Hi, Guys

I probably followed the old version as well. But after the error message, i changed to run:
cds = estimateDispersions(cds)
res = nbinomTest(cds, "T", "N") #T, N two treatments, all of...
Forum: RNA Sequencing 06-18-2013, 09:04 AM
Replies: 10
Views: 2,716
Posted By Baoqing
Thank you, amcloon My programming skill was...

Thank you, amcloon

My programming skill was not good enough to change the setting of the cufflinks, it seems the gene names was the default for the output, or some argument that i have not known...
Forum: RNA Sequencing 06-17-2013, 03:38 PM
Replies: 10
Views: 2,716
Posted By Baoqing
Hi, guys Just wanted to clarify if there is...

Hi, guys

Just wanted to clarify if there is any argument as

“You can run cuffmerge without a "-r <ref.gtf>" but if I do this, will I never have annotations in my later files?”

I looked the...
Forum: Bioinformatics 06-16-2013, 01:24 PM
Replies: 8
Views: 3,604
Posted By Baoqing
Thanks. Still not quite clear to me. Does that...

Thanks. Still not quite clear to me. Does that mean 27,100,851 mRNA, exon or something else? seems unlikely are mRNAs, the read pair examined in total is 6,501,528. Also, it seems that the...
Forum: Bioinformatics 06-16-2013, 09:45 AM
Replies: 8
Views: 3,604
Posted By Baoqing
Interpretation of the PICARD results

Hi, Guys
I was also trying to estimate library complexity with PICARD with my paired end data, I used the tophat aligned reads as input, according to the picard, "One or more files to combine and...
Forum: Bioinformatics 06-12-2013, 12:14 PM
Replies: 21
Views: 11,899
Posted By Baoqing
Ok, problem solved. Two things need to be...

Ok, problem solved.

Two things need to be considered
1 when name your samples "alphabet+ numbers" always help!
2 In case of error, you need to delete cuffData.db in the folder before re-run it.
Forum: Bioinformatics 06-10-2013, 12:29 PM
Replies: 46
Views: 24,843
Posted By Baoqing
awesome. The name sorted bam file worked perfect!...

awesome. The name sorted bam file worked perfect! Really appreciate it!
Forum: Bioinformatics 06-10-2013, 09:34 AM
Replies: 21
Views: 11,899
Posted By Baoqing
Thanks a lot! I will also keep working on...

Thanks a lot!

I will also keep working on mine and keep this post updated periodically.
Forum: Bioinformatics 06-10-2013, 07:26 AM
Replies: 46
Views: 24,843
Posted By Baoqing
Thank you, I did sort my bam files though. I have...

Thank you, I did sort my bam files though. I have the program to finished running, and it turned out a dataset was produced, does that mean everything is good? Should I just ignore the warning...
Forum: Bioinformatics 06-10-2013, 07:18 AM
Replies: 21
Views: 11,899
Posted By Baoqing
Thats cool. But I do have the following up...

Thats cool.

But I do have the following up question though. After load the library(CummeRbund). All of the dependents were loaded simultaneously. I would assume that the package is install...
Forum: Bioinformatics 06-09-2013, 03:04 PM
Replies: 46
Views: 24,843
Posted By Baoqing
sorry, just start to pick up the python, any...

sorry, just start to pick up the python, any reminder message freak me out.

Just set up the path right for htseq-count

then run it with my bam files:
samtools view accepted_hits.bam |...
Forum: Bioinformatics 06-09-2013, 01:39 PM
Replies: 46
Views: 24,843
Posted By Baoqing
HT_SEQ installation

Hi, Simon

I was trying to install HTseq on my local ubuntu machine by following your instruction below:
http://www-huber.embl.de/users/anders/HTSeq/doc/install.html#install

However, there are...
Forum: RNA Sequencing 06-06-2013, 10:32 PM
Replies: 4
Views: 1,210
Posted By Baoqing
Thank you so much! The error does go away when I...

Thank you so much! The error does go away when I rename the "mito" to "MT". It just never came to me that the two files' name are inconsistent. Really appreciate your help!

Baoqing
Forum: RNA Sequencing 06-06-2013, 07:20 AM
Replies: 4
Views: 1,210
Posted By Baoqing
Hi, GenoMax I should have mentioned that i...

Hi, GenoMax

I should have mentioned that i did some initial troubleshooting, you are right that "Mito" is missing in the genome.fa file. It was named as "MT" instead. So I renamed this file, and...
Forum: RNA Sequencing 06-05-2013, 09:06 PM
Replies: 4
Views: 1,210
Posted By Baoqing
cuffmerge error

Hi, All

I was trying to run the cuffmerge for my two samples. However, there is warning message point to the mitochondrial genome, however, i could not figure out the exact problem, could you...
Forum: Bioinformatics 06-05-2013, 05:37 PM
Replies: 21
Views: 11,899
Posted By Baoqing
compiled info to install cummeRbund in ubuntu

wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O R-2.15.0.tar.gz

tar xf R-2.15.0.tar.gz

sudo apt-get install xorg-dev

./configure

make
Forum: Bioinformatics 06-05-2013, 05:20 PM
Replies: 21
Views: 11,899
Posted By Baoqing
ok, problem solved now. I used one of the...

ok, problem solved now.

I used one of the code you gave to other threads

sudo apt-get install libcurl4-openssl-dev

after installation, then reinstall it, now the biocLite("cummeRbund")
is...
Forum: Bioinformatics 06-05-2013, 04:20 PM
Replies: 21
Views: 11,899
Posted By Baoqing
still errors

Hey, guys

I was following your discussion, but still have error messages, could you share some thoughts on this, thanks a lot!
:

wget http://cran.stat.ucla.edu/src/base/R-2/R-2.15.0.tar.gz -O...
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